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Cholera toxin classical B-pentamer in complex with inhibitor PC262
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CHB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M MES/Imidazole pH 6.5, 8% PEG1000, 8% PEG 3350, 8% MPD, 0.03 M divalent cations
Crystal Properties Matthews coefficient Solvent content 2.12 42.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.736 α = 90 b = 66.063 β = 105.67 c = 76.389 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2015-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.991872 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.13 49 73.7 0.073 0.997 6.87 2.8 135800
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.13 1.19 13.9 0.504 0.73 1.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3CHB 1.13 73.55 128966 6823 73.76 0.19895 0.19734 0.22862 0.2266 RANDOM 17.606
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -1.27 0.01 -0.9 1.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.342 r_dihedral_angle_4_deg 21.882 r_dihedral_angle_3_deg 12.476 r_dihedral_angle_1_deg 7.702 r_long_range_B_refined 4.634 r_long_range_B_other 4.633 r_angle_refined_deg 2.501 r_scangle_other 1.841 r_angle_other_deg 1.373 r_scbond_it 1.223
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.342 r_dihedral_angle_4_deg 21.882 r_dihedral_angle_3_deg 12.476 r_dihedral_angle_1_deg 7.702 r_long_range_B_refined 4.634 r_long_range_B_other 4.633 r_angle_refined_deg 2.501 r_scangle_other 1.841 r_angle_other_deg 1.373 r_scbond_it 1.223 r_scbond_other 1.223 r_mcangle_other 1.144 r_mcangle_it 1.143 r_mcbond_it 0.791 r_mcbond_other 0.78 r_chiral_restr 0.155 r_bond_refined_d 0.027 r_gen_planes_refined 0.015 r_bond_other_d 0.006 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4076 Nucleic Acid Atoms Solvent Atoms 608 Heterogen Atoms 241
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing